From owner-chemistry@ccl.net Wed May 24 10:35:01 2006 From: "Konrad Hinsen konrad.hinsen() cea.fr" To: CCL Subject: CCL: DNA modelling (missing atoms in PDB files) Message-Id: <-31824-060524094348-21940-peijPlaOKHMmUHtwjNbSiw---server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Wed, 24 May 2006 09:43:44 -0400 Sent to CCL by: "Konrad Hinsen" [konrad.hinsen:cea.fr] On 24.05.2006, at 14:53, Miro Moman miromoman%a%gmail.com wrote: I am currently modelling protein/DNA complexes. In both protein and DNA structures there are missing atoms/residues. For proteins, I know a number of freely avaliable programs that "guess" the coordinates of the non-resolved atoms and try to reconstruct the structure accordingly (such as SPDBV). However, I could not find any free program able to "correct" the DNA structures in a similar way (the only one I know is LeAP, which comes with the AMBER package). I would very much appreciate any information on such a program. The Molecular Modelling Toolkit (MMTK), available from http://dirac.cnrs-orleans.fr/MMTK/ will do this for proteins, DNA, and most other organic molecules. *However*, it can compute missing coordinates only for hydrogen atoms. -- ------------------------------------------------------------------------------- Konrad Hinsen Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: konrad.hinsen---cea.fr -------------------------------------------------------------------------------